[English] 日本語
Yorodumi
- PDB-6tac: Human NAMPT deletion mutant in complex with nicotinamide mononucl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tac
TitleHuman NAMPT deletion mutant in complex with nicotinamide mononucleotide, pyrophosphate, and Mg2+
ComponentsNicotinamide phosphoribosyltransferase
KeywordsTRANSFERASE / NAD biosynthesis / substrate complex
Function / homology
Function and homology information


nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / NAD biosynthetic process / positive regulation of nitric-oxide synthase biosynthetic process / NPAS4 regulates expression of target genes / BMAL1:CLOCK,NPAS2 activates circadian gene expression / cytokine activity / circadian regulation of gene expression ...nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / NAD biosynthetic process / positive regulation of nitric-oxide synthase biosynthetic process / NPAS4 regulates expression of target genes / BMAL1:CLOCK,NPAS2 activates circadian gene expression / cytokine activity / circadian regulation of gene expression / cell junction / cell-cell signaling / nuclear speck / positive regulation of cell population proliferation / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / cytosol
Similarity search - Function
Nicotinamide phosphoribosyl transferase / Nicotinamide phosphoribosyltransferase, N-terminal domain / Nicotinamide phosphoribosyltransferase, N-terminal domain / Nicotinate/nicotinamide phosphoribosyltransferase / Nicotinate phosphoribosyltransferase (NAPRTase) family / Nicotinate phosphoribosyltransferase-like, C-terminal / Aldolase-type TIM barrel
Similarity search - Domain/homology
BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / PYROPHOSPHATE / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHoury, D. / Raasakka, A. / Kursula, P. / Ziegler, M.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway810882 Norway
CitationJournal: To Be Published
Title: Identification of structural determinants of NAMPT activity and substrate selectivity
Authors: Houry, D. / Raasakka, A. / Kursula, P. / Ziegler, M.
History
DepositionOct 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nicotinamide phosphoribosyltransferase
B: Nicotinamide phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,78011
Polymers111,5642
Non-polymers1,2169
Water20,7711153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11410 Å2
ΔGint-81 kcal/mol
Surface area32130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.017, 106.666, 83.549
Angle α, β, γ (deg.)90.000, 96.623, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Nicotinamide phosphoribosyltransferase / / Nampt / Pre-B-cell colony-enhancing factor 1 / Pre-B cell-enhancing factor / Visfatin


Mass: 55782.004 Da / Num. of mol.: 2 / Mutation: deletion of residues 42-51
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAMPT, PBEF, PBEF1 / Production host: Escherichia coli (E. coli)
References: UniProt: P43490, nicotinamide phosphoribosyltransferase

-
Non-polymers , 5 types, 1162 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE / Nicotinamide mononucleotide


Mass: 335.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N2O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PPV / PYROPHOSPHATE / Pyrophosphate


Mass: 177.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1153 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Bis Tris propane, 200 mM NaF, 16% PEG3350, 10 mM Nam, 10 mM PRPP, 6 mM MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. obs: 138876 / % possible obs: 99.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 17.83 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.07 / Rrim(I) all: 0.104 / Net I/σ(I): 8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 6869 / CC1/2: 0.637 / Rpim(I) all: 0.586 / Rrim(I) all: 0.884 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3dhd

3dhd


Resolution: 1.6→60.61 Å / SU ML: 0.154 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.3124
RfactorNum. reflection% reflection
Rfree0.1708 6908 4.98 %
Rwork0.1427 --
obs0.1441 138823 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→60.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7472 0 72 1153 8697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00897875
X-RAY DIFFRACTIONf_angle_d1.032510707
X-RAY DIFFRACTIONf_chiral_restr0.05831167
X-RAY DIFFRACTIONf_plane_restr0.00731368
X-RAY DIFFRACTIONf_dihedral_angle_d16.9344672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.27912080.25164377X-RAY DIFFRACTION99.54
1.62-1.640.29162550.23824378X-RAY DIFFRACTION99.25
1.64-1.660.24012220.22734359X-RAY DIFFRACTION98.77
1.66-1.680.27482270.22534290X-RAY DIFFRACTION97.27
1.68-1.70.22192460.2134403X-RAY DIFFRACTION99.94
1.7-1.720.23892080.19714404X-RAY DIFFRACTION99.91
1.72-1.750.22151920.18354480X-RAY DIFFRACTION99.94
1.75-1.770.2192380.17964378X-RAY DIFFRACTION99.94
1.77-1.80.23292550.1794381X-RAY DIFFRACTION99.91
1.8-1.830.21712330.17364418X-RAY DIFFRACTION99.87
1.83-1.860.21652460.16864357X-RAY DIFFRACTION99.87
1.86-1.90.20392250.16854418X-RAY DIFFRACTION99.83
1.9-1.930.20052210.15664382X-RAY DIFFRACTION99.5
1.93-1.970.19582180.15054432X-RAY DIFFRACTION99.51
1.97-2.020.19182290.15084327X-RAY DIFFRACTION98.25
2.02-2.060.17742140.14054415X-RAY DIFFRACTION99.81
2.06-2.110.17122160.13834453X-RAY DIFFRACTION99.83
2.11-2.170.15112300.13164400X-RAY DIFFRACTION99.85
2.17-2.240.15492450.12984367X-RAY DIFFRACTION99.68
2.24-2.310.16862510.12754397X-RAY DIFFRACTION99.83
2.31-2.390.16552570.12774382X-RAY DIFFRACTION99.61
2.39-2.490.14772300.1234386X-RAY DIFFRACTION99.35
2.49-2.60.1592310.12794381X-RAY DIFFRACTION98.5
2.6-2.740.16132430.1224408X-RAY DIFFRACTION99.68
2.74-2.910.16952260.12954420X-RAY DIFFRACTION99.74
2.91-3.130.1472110.13124429X-RAY DIFFRACTION99.49
3.13-3.450.17782320.13254396X-RAY DIFFRACTION99.04
3.45-3.950.13192530.1274323X-RAY DIFFRACTION97.8
3.95-4.970.12452310.11444461X-RAY DIFFRACTION99.79
4.97-60.610.18522150.16074513X-RAY DIFFRACTION99.14

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more